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Asym./Biol. Unit (Jmol Viewer)

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Title :   IN VITRO AND IN VIVO INHIBITION OF HUMAN D-AMINO ACID OXIDASE: REGULATION OF D-SERINE CONCENTRATION IN THE BRAIN

Authors :   S. C. Hopkins, M. L. R. Heffernan, L. D. Saraswat, C. A. Bowen, L. Melnick L. W. Hardy, M. A. Orsini, M. S. Allen, P. Koch, K. L. Spear, R. J. Fogleso M. Soukri, M. Chytil, Q. K. Fang, S. W. Jones, M. A. Varney, A. Panatier, S. H. R. Oliet, L. Pollegioni, L. Piubelli, G. Molla, M. Nardini, T. H. L

Date :   15 Feb 13 (Deposition) - 15 May 13 (Release) - 22 May 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.90

Chains :   Asym./Biol. Unit : A,B

Keywords :   Oxidoreductase, Flavooxidase, Neurotransmission (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. C. Hopkins, M. L. R. Heffernan, L. D. Saraswat, C. A. Bowen, L. Melnick, L. W. Hardy, M. A. Orsini, M. S. Allen, P. Koch, K. L. Spear, R. J. Foglesong, M. Soukri, M. Chytil, Q. K. Fang, S. W. Jones, M. A. Varney, A. Panatier, S. H. R. Oliet, L. Pollegioni, L. Piubelli, G. Molla, M. Nardini, T. H. Large
Structural, Kinetic, And Pharmacodynamic Mechanisms Of D- Amino Acid Oxidase Inhibition By Small Molecules.
J. Med. Chem. V. 56 3710 2013
PubMed-ID: 23631755 | Reference-DOI: 10.1021/JM4002583

Molecule 1 - D-AMINO-ACID OXIDASE
	Chains	:	A, B
	EC Number	:	1.4.3.3
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	DAAO, DAMOX, DAO, D-AMINO ACID OXIDASE

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (3, 15)

No.	Name	Count	Type	Full Name
1	4WL	2	Ligand/Ion	4H-THIENO[3,2-B]PYROLE-5-CARBOXYLIC ACID
2	FAD	2	Ligand/Ion	FLAVIN-ADENINE DINUCLEOTIDE
3	GOL	11	Ligand/Ion	GLYCEROL

Asymmetric Unit (15, 15)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	GLY A:7 , ALA A:8 , GLY A:9 , VAL A:10 , ILE A:11 , ALA A:36 , ASP A:37 , ARG A:38 , THR A:43 , THR A:44 , THR A:45 , ALA A:48 , ALA A:49 , GLY A:50 , LEU A:51 , ARG A:162 , LYS A:163 , VAL A:164 , CYS A:181 , THR A:182 , GLY A:183 , TRP A:185 , ILE A:202 , TYR A:228 , ARG A:283 , HIS A:311 , GLY A:312 , GLY A:313 , TYR A:314 , GLY A:315 , LEU A:316 , THR A:317 , 4WL A:360 , GOL A:1343 , HOH A:2011 , HOH A:2016 , HOH A:2048 , HOH A:2094	BINDING SITE FOR RESIDUE FAD A 350
02	AC2	SOFTWARE	LEU A:51 , TYR A:224 , TYR A:228 , ILE A:230 , ARG A:283 , GLY A:313 , FAD A:350 , GOL A:1345	BINDING SITE FOR RESIDUE 4WL A 360
03	AC3	SOFTWARE	GLY B:7 , ALA B:8 , GLY B:9 , VAL B:10 , ILE B:11 , ALA B:36 , ASP B:37 , ARG B:38 , THR B:43 , THR B:44 , THR B:45 , ALA B:48 , ALA B:49 , GLY B:50 , LEU B:51 , ARG B:162 , VAL B:164 , CYS B:181 , THR B:182 , GLY B:183 , TRP B:185 , ILE B:202 , TYR B:228 , ARG B:283 , GLY B:312 , GLY B:313 , TYR B:314 , GLY B:315 , LEU B:316 , THR B:317 , 4WL B:360 , HOH B:2029 , HOH B:2058 , HOH B:2060 , HOH B:2062 , HOH B:2078	BINDING SITE FOR RESIDUE FAD B 350
04	AC4	SOFTWARE	LEU B:51 , GLN B:53 , TYR B:224 , TYR B:228 , ILE B:230 , ARG B:283 , GLY B:313 , FAD B:350	BINDING SITE FOR RESIDUE 4WL B 360
05	AC5	SOFTWARE	LYS A:158 , PHE A:159 , PHE A:160	BINDING SITE FOR RESIDUE GOL A1341
06	AC6	SOFTWARE	PRO B:193 , LEU B:194 , GLN B:196 , PRO B:287 , HOH B:2145	BINDING SITE FOR RESIDUE GOL B1341
07	AC7	SOFTWARE	PHE A:98 , HIS A:99 , GLU A:100 , ILE A:102 , HIS A:217 , PRO A:219 , HOH A:2073	BINDING SITE FOR RESIDUE GOL A1342
08	AC8	SOFTWARE	PRO A:300 , GLY B:187 , ARG B:191 , ASP B:192 , PRO B:193 , LEU B:339	BINDING SITE FOR RESIDUE GOL B1342
09	AC9	SOFTWARE	ASP A:37 , ARG A:38 , LYS A:163 , TRP A:185 , FAD A:350 , GOL A:1346 , HOH A:2085	BINDING SITE FOR RESIDUE GOL A1343
10	BC1	SOFTWARE	THR A:45 , ASP A:46 , ALA A:48 , ALA A:49 , GLU A:140 , GLY A:141 , LYS A:142 , LYS A:204	BINDING SITE FOR RESIDUE GOL A1344
11	BC2	SOFTWARE	GLN A:53 , PRO A:54 , LEU A:56 , HIS A:217 , 4WL A:360 , HOH A:2068 , HOH A:2123	BINDING SITE FOR RESIDUE GOL A1345
12	BC3	SOFTWARE	TRP A:185 , TRP A:247 , GLU A:249 , PHE A:282 , GOL A:1343	BINDING SITE FOR RESIDUE GOL A1346
13	BC4	SOFTWARE	HIS B:99 , ASP B:127 , TYR B:128 , GLY B:129 , HOH B:2031 , HOH B:2081	BINDING SITE FOR RESIDUE GOL B1343
14	BC5	SOFTWARE	HIS A:80 , ASP B:123 , MET B:124 , PRO B:126	BINDING SITE FOR RESIDUE GOL B1344
15	BC6	SOFTWARE	GLU A:294 , GLN A:295	BINDING SITE FOR RESIDUE GOL A1347

(no "SS Bond" information available for 3ZNN)

Asymmetric/Biological Unit

No.	Residues
1	Thr A:40	-	Pro A:41
2	Thr B:40	-	Pro B:41

(no "SAP(SNP)/Variant" information available for 3ZNN)

Asymmetric/Biological Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	DAO	PS00677	D-amino acid oxidases signature.	OXDA_HUMAN	305-323	2	A:305-323 B:305-323

Asymmetric/Biological Unit (10, 20)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	ENST00000228476	1	ENSE00001232085	chr12:109273857-109274000	144	OXDA_HUMAN	-	0	0	-	-
1.2	ENST00000228476	2	ENSE00001232101	chr12:109278774-109278976	203	OXDA_HUMAN	1-65	65	2	A:1-65 B:1-65	65 65
1.3	ENST00000228476	3	ENSE00001232078	chr12:109281226-109281340	115	OXDA_HUMAN	65-103	39	2	A:65-103 B:65-103	39 39
1.4	ENST00000228476	4	ENSE00001232074	chr12:109283245-109283321	77	OXDA_HUMAN	104-129	26	2	A:104-129 B:104-129	26 26
1.5	ENST00000228476	5	ENSE00001232068	chr12:109283984-109284049	66	OXDA_HUMAN	129-151	23	2	A:129-151 B:129-151	23 23
1.6	ENST00000228476	6	ENSE00001232066	chr12:109286758-109286812	55	OXDA_HUMAN	151-169	19	2	A:151-169 B:151-169	19 19
1.7	ENST00000228476	7	ENSE00001232061	chr12:109288039-109288143	105	OXDA_HUMAN	170-204	35	2	A:170-204 B:170-204	35 35
1.8	ENST00000228476	8	ENSE00000754687	chr12:109290782-109290864	83	OXDA_HUMAN	205-232	28	2	A:205-232 B:205-232	28 28
1.9	ENST00000228476	9	ENSE00001232053	chr12:109292455-109292572	118	OXDA_HUMAN	232-271	40	2	A:232-271 B:232-271	40 40
1.10	ENST00000228476	10	ENSE00001232046	chr12:109293153-109293251	99	OXDA_HUMAN	272-304	33	2	A:272-304 B:272-304	33 33
1.11	ENST00000228476	11	ENSE00001232095	chr12:109294180-109294709	530	OXDA_HUMAN	305-347	43	2	A:305-340 B:305-340	36 36

Asymmetric/Biological Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
	Number of residues per labelling interval =
	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
	(details for a mapped element are shown in a popup box when the mouse pointer rests over it)

Chain A from PDB  Type:PROTEIN  Length:340
 aligned with OXDA_HUMAN | P14920 from UniProtKB/Swiss-Prot  Length:347

    Alignment length:340
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340
           OXDA_HUMAN     1 MRVVVIGAGVIGLSTALCIHERYHSVLQPLDIKVYADRFTPLTTTDVAAGLWQPYLSDPNNPQEADWSQQTFDYLLSHVHSPNAENLGLFLISGYNLFHEAIPDPSWKDTVLGFRKLTPRELDMFPDYGYGWFHTSLILEGKNYLQWLTERLTERGVKFFQRKVESFEEVAREGADVIVNCTGVWAGALQRDPLLQPGRGQIMKVDAPWMKHFILTHDPERGIYNSPYIIPGTQTVTLGGIFQLGNWSELNNIQDHNTIWEGCCRLEPTLKNARIIGERTGFRPVRPQIRLEREQLRTGPSNTEVIHNYGHGGYGLTIHWGCALEAAKLFGRILEEKKLS 340
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee..hhhhhhhhhhhhhhhh......eeeeee......hhhhhh.............hhhhhhhhhhhhhhhhh....hhhhhheeeeeeeeee.............eeeee.hhhhhh......eeeeeeeeeehhhhhhhhhhhhhhhh..eeee....hhhhhhhh...eeee.hhhhhhhh......eeeeeeeeeee......eeee...........eeee....eeee...ee.......hhhhhhhhhhhhhhhhhhhhhheeeeeeeeeeee....eeeeeee......eeeeeee....hhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------DAO  PDB: A:305-323----------------- PROSITE
           Transcript 1 (1) Exon 1.2  PDB: A:1-65 UniProt: 1-65                              --------------------------------------Exon 1.4  PDB: A:104-129  ---------------------Exon 1.6           Exon 1.7  PDB: A:170-204           Exon 1.8  PDB: A:205-232    ---------------------------------------Exon 1.10  PDB: A:272-304        Exon 1.11  PDB: A:305-340            Transcript 1 (1)
           Transcript 1 (2) ----------------------------------------------------------------Exon 1.3  PDB: A:65-103 UniProt: 65-103-------------------------Exon 1.5  PDB: A:129-15--------------------------------------------------------------------------------Exon 1.9  PDB: A:232-271                --------------------------------------------------------------------- Transcript 1 (2)
                 3znn A   1 MRVVVIGAGVIGLSTALCIHERYHSVLQPLDIKVYADRFTPLTTTDVAAGLWQPYLSDPNNPQEADWSQQTFDYLLSHVHSPNAENLGLFLISGYNLFHEAIPDPSWKDTVLGFRKLTPRELDMFPDYGYGWFHTSLILEGKNYLQWLTERLTERGVKFFQRKVESFEEVAREGADVIVNCTGVWAGALQRDPLLQPGRGQIMKVDAPWMKHFILTHDPERGIYNSPYIIPGTQTVTLGGIFQLGNWSELNNIQDHNTIWEGCCRLEPTLKNARIIGERTGFRPVRPQIRLEREQLRTGPSNTEVIHNYGHGGYGLTIHWGCALEAAKLFGRILEEKKLS 340
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340

Chain B from PDB  Type:PROTEIN  Length:340
 aligned with OXDA_HUMAN | P14920 from UniProtKB/Swiss-Prot  Length:347

    Alignment length:340
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340
           OXDA_HUMAN     1 MRVVVIGAGVIGLSTALCIHERYHSVLQPLDIKVYADRFTPLTTTDVAAGLWQPYLSDPNNPQEADWSQQTFDYLLSHVHSPNAENLGLFLISGYNLFHEAIPDPSWKDTVLGFRKLTPRELDMFPDYGYGWFHTSLILEGKNYLQWLTERLTERGVKFFQRKVESFEEVAREGADVIVNCTGVWAGALQRDPLLQPGRGQIMKVDAPWMKHFILTHDPERGIYNSPYIIPGTQTVTLGGIFQLGNWSELNNIQDHNTIWEGCCRLEPTLKNARIIGERTGFRPVRPQIRLEREQLRTGPSNTEVIHNYGHGGYGLTIHWGCALEAAKLFGRILEEKKLS 340
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee..hhhhhhhhhhhhhhhh......eeeeee......hhhhh..............hhhhhhhhhhhhhhhhhh...hhhhhheeeeeeeeee.............eeeee.hhhhhh......eeeeeeeeeehhhhhhhhhhhhhhh...eeee....hhhhhhhh...eeee.hhhhhhhh......eeeeeeeeeee......eeee...........eeee....eeee...ee.......hhhhhhhhhhhhhhhhhhhhhheeeeeeeeeeee....eeeeee........eeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------DAO  PDB: B:305-323----------------- PROSITE
           Transcript 1 (1) Exon 1.2  PDB: B:1-65 UniProt: 1-65                              --------------------------------------Exon 1.4  PDB: B:104-129  ---------------------Exon 1.6           Exon 1.7  PDB: B:170-204           Exon 1.8  PDB: B:205-232    ---------------------------------------Exon 1.10  PDB: B:272-304        Exon 1.11  PDB: B:305-340            Transcript 1 (1)
           Transcript 1 (2) ----------------------------------------------------------------Exon 1.3  PDB: B:65-103 UniProt: 65-103-------------------------Exon 1.5  PDB: B:129-15--------------------------------------------------------------------------------Exon 1.9  PDB: B:232-271                --------------------------------------------------------------------- Transcript 1 (2)
                 3znn B   1 MRVVVIGAGVIGLSTALCIHERYHSVLQPLDIKVYADRFTPLTTTDVAAGLWQPYLSDPNNPQEADWSQQTFDYLLSHVHSPNAENLGLFLISGYNLFHEAIPDPSWKDTVLGFRKLTPRELDMFPDYGYGWFHTSLILEGKNYLQWLTERLTERGVKFFQRKVESFEEVAREGADVIVNCTGVWAGALQRDPLLQPGRGQIMKVDAPWMKHFILTHDPERGIYNSPYIIPGTQTVTLGGIFQLGNWSELNNIQDHNTIWEGCCRLEPTLKNARIIGERTGFRPVRPQIRLEREQLRTGPSNTEVIHNYGHGGYGLTIHWGCALEAAKLFGRILEEKKLS 340
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
		→ Modified Residue	(blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
	x	→ Chemical Group	(purple background, 'x', labelled with number + name, e.g. ACE or NH2)
	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

(no "SCOP Domain" information available for 3ZNN)

(no "CATH Domain" information available for 3ZNN)

(no "Pfam Domain" information available for 3ZNN)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (OXDA_HUMAN | P14920)

molecular function
	GO:0003884	D-amino-acid oxidase activity	Catalysis of the reaction: a D-amino acid + H2O + O2 = a 2-oxo acid + NH3 + hydrogen peroxide.
	GO:0071949	FAD binding	Interacting selectively and non-covalently with the oxidized form, FAD, of flavin-adenine dinucleotide, the coenzyme or the prosthetic group of various flavoprotein oxidoreductase enzymes.
	GO:0048037	cofactor binding	Interacting selectively and non-covalently with a cofactor, a substance that is required for the activity of an enzyme or other protein. Cofactors may be inorganic, such as the metal atoms zinc, iron, and copper in certain forms, or organic, in which case they are referred to as coenzymes. Cofactors may either be bound tightly to active sites or bind loosely with the substrate.
	GO:0016491	oxidoreductase activity	Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
	GO:0046983	protein dimerization activity	The formation of a protein dimer, a macromolecular structure consists of two noncovalently associated identical or nonidentical subunits.
	GO:0005102	receptor binding	Interacting selectively and non-covalently with one or more specific sites on a receptor molecule, a macromolecule that undergoes combination with a hormone, neurotransmitter, drug or intracellular messenger to initiate a change in cell function.
biological process
	GO:0055130	D-alanine catabolic process	The chemical reactions and pathways resulting in the breakdown of D-alanine, the D-enantiomer of the amino acid alanine.
	GO:0046416	D-amino acid metabolic process	The chemical reactions and pathways involving D-amino acids, the D-enantiomers of amino acids.
	GO:0036088	D-serine catabolic process	The chemical reactions and pathways resulting in the breakdown of D-serine, the D-enantiomer of serine, i.e. (2S)-2-amino-3-hydroxypropanoic acid.
	GO:0070178	D-serine metabolic process	The chemical reactions and pathways involving D-serine, the D-enantiomer of serine, i.e. (2R)-2-amino-3-hydroxypropanoic acid.
	GO:0042416	dopamine biosynthetic process	The chemical reactions and pathways resulting in the formation of dopamine, a catecholamine neurotransmitter and a metabolic precursor of noradrenaline and adrenaline.
	GO:0046487	glyoxylate metabolic process	The chemical reactions and pathways involving glyoxylate, the anion of glyoxylic acid, HOC-COOH.
	GO:0055114	oxidation-reduction process	A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
	GO:0006562	proline catabolic process	The chemical reactions and pathways resulting in the breakdown of proline (pyrrolidine-2-carboxylic acid), a chiral, cyclic, nonessential alpha-amino acid found in peptide linkage in proteins.
cellular component
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
	GO:0005741	mitochondrial outer membrane	The outer, i.e. cytoplasm-facing, lipid bilayer of the mitochondrial envelope.
	GO:0005782	peroxisomal matrix	The volume contained within the membranes of a peroxisome; in many cells the matrix contains a crystalloid core largely composed of urate oxidase.
	GO:0005778	peroxisomal membrane	The lipid bilayer surrounding a peroxisome.
	GO:0005777	peroxisome	A small organelle enclosed by a single membrane, and found in most eukaryotic cells. Contains peroxidases and other enzymes involved in a variety of metabolic processes including free radical detoxification, lipid catabolism and biosynthesis, and hydrogen peroxide metabolism.

Asymmetric/Biological Unit
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	3znn
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	OXDA_HUMAN \| P14920
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3zno	IN VITRO AND IN VIVO INHIBITION OF HUMAN D-AMINO ACID OXIDASE: REGULATION OF D-SERINE CONCENTRATION IN THE BRAIN
3znp	IN VITRO AND IN VIVO INHIBITION OF HUMAN D-AMINO ACID OXIDASE: REGULATION OF D-SERINE CONCENTRATION IN THE BRAIN
3znq	IN VITRO AND IN VIVO INHIBITION OF HUMAN D-AMINO ACID OXIDASE: REGULATION OF D-SERINE CONCENTRATION IN THE BRAIN

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 15)

Sites (15, 15)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 2)

Exons (10, 20)

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Gene Ontology (20, 20)

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